Hello, Does anyone know why gcrma wouldn't work with the moe chips when it works for the mgu74av2 chipset? Any input is appreciated. the output is: WORKS! > gcrmadata<-gcrma(gcdata) Loading required package: mgu74av2probe Loading required package: matchprobes background correction: gcrma normalization: quantiles PM/MM correction : pmonly expression values: medianpolish background correcting...done. normalizing...done. 12488 ids to be processed ......... ???? > gcrmadata<-gcrma(data) Loading required package: moe430bprobe Loading required package: matchprobes background correction: gcrma normalization: quantiles PM/MM correction : pmonly expression values: medianpolish background correcting...done. normalizing...Error in as.vector(data) : NA/NaN/Inf in foreign function call (arg 1) best, michael Michael J. McDonald Ph.D. Universite de Geneve c/o Duboule Lab Department of Zoologie and Biologie Animale Quai Ernest-Ansermet 30 CH-1211 Geneve 4 phone 41.22.379.67.94 fax 41.22.379.67.95

HI, there is a bug in matching the probe sequence and the intensities from the pm function for certain types of chips. We will release the updated version soon. For now, please source the attached .r file after you load library(gcrma) for a quick fix. Jean On Mon, 15 Sep 2003, Michael McDonald wrote: > Hello, > Does anyone know why gcrma wouldn't work with the moe chips when it > works for the mgu74av2 chipset? Any input is appreciated. the output > is: > WORKS! > > gcrmadata<-gcrma(gcdata) > Loading required package: mgu74av2probe > Loading required package: matchprobes > background correction: gcrma > normalization: quantiles > PM/MM correction : pmonly > expression values: medianpolish > background correcting...done. > normalizing...done. > 12488 ids to be processed > ......... > > > ???? > > gcrmadata<-gcrma(data) > Loading required package: moe430bprobe > Loading required package: matchprobes > background correction: gcrma > normalization: quantiles > PM/MM correction : pmonly > expression values: medianpolish > background correcting...done. > normalizing...Error in as.vector(data) : NA/NaN/Inf in foreign function > call (arg 1) > > best, > michael > > Michael J. McDonald Ph.D. > Universite de Geneve c/o Duboule Lab > Department of Zoologie and Biologie Animale > Quai Ernest-Ansermet 30 > CH-1211 Geneve 4 > phone 41.22.379.67.94 > fax 41.22.379.67.95 > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > -------------- next part -------------- getGroupInfo<- function(object){ allprobes<-probeNames(object) matchaffyName=paste(cleancdfname(object@cdfName,addcdf=FALSE),"probe ",sep="") if (identical(.find.package(matchaffyName, quiet=TRUE),character(0))) stop(paste("Probe sequence information not available. Please download and install the",matchaffyName,"library from:\n http://www.bioconductor.org/data/metaData.html\n See the vignette of matchprobes and gcrma for more details")) require(matchaffyName,character.only = TRUE) seqData <- get(matchaffyName) ##check seqData t1=table(allprobes);t2=table(seqData$Probe.Set) good.set=names(t1)[which(t2[names(t1)]==t1)]##probesets with complete probe seq info good.probe=which(seqData$Probe.Set.Name%in%good.set) mm.seq<- complementSeq(seqData$seq[good.probe],start=13,stop=13) ATCGmm=basecontent(mm.seq) CGadj=ATCGmm[,3:4] CGadj[CGadj<=4]=4 CGadj[CGadj>=8]=8 Index2=which(allprobes%in%good.set) #probes with seq group2d=as.list(NULL) for (C in 4:8) { for(G in 4:8) {group2d=c(group2d,list(Index2[which(CGadj[,1]==C & CGadj[,2]==G)]))}} c(group2d,list(which(!allprobes%in%good.set))) }

We've just updated the gcrma package. The bug due to sequence matching mistake has been fixed. Thanks to Akil Merchant and Michael McDonald who brought it to our attention, and thank Wolfgang for explaining the precise way of matching those! Jean On Mon, 15 Sep 2003, Michael McDonald wrote: > Hello, > Does anyone know why gcrma wouldn't work with the moe chips when it > works for the mgu74av2 chipset? Any input is appreciated. the output > is: > WORKS! > > gcrmadata<-gcrma(gcdata) > Loading required package: mgu74av2probe > Loading required package: matchprobes > background correction: gcrma > normalization: quantiles > PM/MM correction : pmonly > expression values: medianpolish > background correcting...done. > normalizing...done. > 12488 ids to be processed > ......... > > > ???? > > gcrmadata<-gcrma(data) > Loading required package: moe430bprobe > Loading required package: matchprobes > background correction: gcrma > normalization: quantiles > PM/MM correction : pmonly > expression values: medianpolish > background correcting...done. > normalizing...Error in as.vector(data) : NA/NaN/Inf in foreign function > call (arg 1) > > best, > michael > > Michael J. McDonald Ph.D. > Universite de Geneve c/o Duboule Lab > Department of Zoologie and Biologie Animale > Quai Ernest-Ansermet 30 > CH-1211 Geneve 4 > phone 41.22.379.67.94 > fax 41.22.379.67.95 > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor >